Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_013842340.1 DESRU_RS11830 aspartate carbamoyltransferase catalytic subunit
Query= curated2:Q3A9W4 (311 letters) >NCBI__GCF_000215085.1:WP_013842340.1 Length = 312 Score = 140 bits (354), Expect = 3e-38 Identities = 107/313 (34%), Positives = 162/313 (51%), Gaps = 17/313 (5%) Query: 5 YRGRDFLSMNDLTGEEIEEVLDLASELK-IRQKKGISTPILKGKTLAMIFSKNSTRTRVS 63 ++ +D L + DLT EEI +LD A +K I +K TP L+G+++ +F +NSTRTR S Sbjct: 3 WQRKDLLGLRDLTAEEISLILDTAVPMKGIIGRKIKKTPTLRGRSVVTLFYENSTRTRSS 62 Query: 64 FEVGMVQLGGYPLFITATDSQLSRGEPIADTARVLSRM-VDGIMIRTYSHSEVEELAYYA 122 F++ L + ++A+ S +++GE + DT L+ M VD ++IR + E LA Sbjct: 63 FDLAAKFLSADTVGLSASSSSVAKGESLRDTGLTLNAMGVDVVVIRHPASGAAEYLARCI 122 Query: 123 DVPVIN-GLTDYEHPCQIMADLLTIKEHKGQLRGLKVAWVGD--GNNVCHSLMIGAAKVG 179 VIN G +EHP Q + DL TI+E KG L GLKVA VGD + V S + G K+G Sbjct: 123 PAAVINAGDGTHEHPTQALLDLFTIREKKGTLTGLKVAIVGDILHSRVARSNIWGLTKMG 182 Query: 180 MEVAVATPPGYEPDQKVSLIAQKETSRWGTKLLLTHDPVEAVTGADVV-VTDVWASMGQE 238 EV V+ P S + + + G K+ D A+ GADVV + + Q+ Sbjct: 183 AEVRVSGP---------STLMPPDIEQMGVKVYSELD--AALEGADVVNMLRIQLERQQQ 231 Query: 239 AESAERVKVFEPYQVNGELVSHAKQDFIFLHCLPAHRGEEVTAEVIDGEHSVVFAEAENR 298 + + +N + D + LH P +RG E++AEV G SV+ + N Sbjct: 232 GLFPSIREYSRLFGMNQRRLELTAPDALVLHPGPINRGVEISAEVAYGSRSVILDQVTNG 291 Query: 299 LHAQKAILTLLLG 311 + + A+L LL G Sbjct: 292 VAVRMALLYLLTG 304 Lambda K H 0.317 0.134 0.382 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 198 Number of extensions: 11 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 311 Length of database: 312 Length adjustment: 27 Effective length of query: 284 Effective length of database: 285 Effective search space: 80940 Effective search space used: 80940 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory